Laser ablation is nowadays an extensively applied technology to probe the chemical composition of solid materials. It allows for precise targeting of micrometer objects on and in samples, and enables chemical depth profiling with nanometer resolution. An in-depth understanding of the 3D geometry of the ablation craters is crucial for precise calibration of the depth scale in chemical depth profiles. Herein we present a comprehensive study on laser ablation processes using a Gaussian-shaped UV-femtosecond irradiation source and present how the combination of three different imaging methods (scanning electron microscopy, interferometric microscopy, and X-ray computed tomography) can provide accurate information on the crater’s shapes. Crater analysis by applying X-ray computed tomography is of considerable interest because it allows the imaging of an array of craters in one step with sub-µm accuracy and is not limited to the aspect ratio of the crater. X-ray computed tomography thereby complements the analysis of laser ablation craters. The study investigates the effect of laser pulse energy and laser burst count on a single crystal Ru(0001) sample. Single crystals ensure that there is no dependence on the grain orientations during the laser ablation process. An array of 156 craters of different dimensions ranging from <20 nm to ∼40 µm in depth were created. For each individually applied laser pulse, we measured the number of ions generated in the ablation plume with our laser ablation ionization mass spectrometer. We show to which extent the combination of these four techniques reveals valuable information on the ablation threshold, the ablation rate, and the limiting ablation depth. The latter is expected to be a consequence of decreasing irradiance upon increasing crater surface area. The ion signal generated was found to be proportional to the volume ablated up to the certain depth, which enables in-situ depth calibration during the measurement.